'\" t
.TH samtools-rmdup 1 "14 July 2025" "samtools-1.22.1" "Bioinformatics tools"
.SH NAME
samtools rmdup \- removes duplicate reads (obsolete)
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
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.
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.SH SYNOPSIS
.PP
samtools rmdup
.RB [ -sS ]
.I input.srt.bam out.bam

.SH DESCRIPTION
.PP
.B This command is obsolete.  Use markdup instead.

Remove potential PCR duplicates: if multiple read pairs have identical
external coordinates, only retain the pair with highest mapping quality.
In the paired-end mode, this command
.B ONLY
works with FR orientation and requires ISIZE is correctly set. It does
not work for unpaired reads (e.g. two ends mapped to different
chromosomes or orphan reads).

.SH OPTIONS
.TP 8
.B -s
Remove duplicates for single-end reads. By default, the command works for
paired-end reads only.
.TP 8
.B -S
Treat paired-end reads and single-end reads.

.SH LIMITATIONS
.IP o 2
Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan
reads or ends mapped to different chromosomes). If this is a concern,
please use Picard's MarkDuplicates which correctly handles these cases,
although a little slower.

.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
